Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors

Article abstract of DOI:10.1021/acs.jmedchem.9b00686

Drug discovery programs of covalent irreversible, mechanism-based enzyme inhibitors often focus on optimization of potency as determined by IC₅₀-values in biochemical assays. These assays do not allow the characterization of the binding activity (K_i) and reactivity (k_inact) as individual kinetic parameters of the covalent inhibitors. Here, we report the development of a kinetic substrate assay to study the influence of the acidity (pK_a) of heterocyclic leaving group of triazole urea derivatives as diacylglycerol lipase (DAGL)-α inhibitors. Surprisingly, we found that the reactivity of the inhibitors did not correlate with the pK_a of the leaving group, whereas the position of the nitrogen atoms in the heterocyclic core determined to a large extent the binding activity of the inhibitor. This finding was confirmed and clarified by molecular dynamics simulations on the covalently bound Michaelis-Menten complex. A deeper understanding of the binding properties of covalent serine hydrolase inhibitors is expected to aid in the discovery and development of more selective covalent inhibitors.

Full text of DOI:10.1021/acs.jmedchem.9b00686

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Article
Structure Kinetics Relationships and Molecular Dynamics show crucial role
for heterocycle leaving group in irreversible diacylglycerol lipase inhibitors
Antonius P.A. Janssen, Jacob van Hengst, Olivier Béquignon,
Hui Deng, Gerard van Westen, and Mario van der Stelt
J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.9b00686 • Publication Date (Web): 22 Aug 2019
Downloaded from pubs.acs.org on August 23, 2019
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Structure Kinetics Relationships and Molecular Dynamics show crucial role for heterocycle
leaving group in irreversible diacylglycerol lipase inhibitors
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Antonius P.A. Janssen1, Jacob M.A. van Hengst1, Olivier J.M. Béquignon2, Hui Deng1, Gerard J.P. van
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Westen2, Mario van der Stelt1*
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1 Molecular Physiology, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300RA Leiden, The
Netherlands
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Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O.
Box 9502, 2300 RA, Leiden, The Netherlands
Abstract
Drug discovery programs of covalent irreversible, mechanism-based enzyme inhibitors often focus on
optimization of potency as determined by IC50-values in biochemical assays. These assays do not allow
the characterisation of the binding activity (Ki) and reactivity (kinact) as individual kinetic parameters of
the covalent inhibitors. Here, we report the development of a kinetic substrate assay to study the
influence of the acidity (pKa) of heterocyclic leaving group of triazole urea derivatives as diacylglycerol
lipase (DAGL)-α inhibitors. Surprisingly, we found that the reactivity of the inhibitors did not correlate
with the pKa of the leaving group, whereas the position of the nitrogen atoms in the heterocyclic core
determined to a large extent the binding activity of the inhibitor. This finding was confirmed and
clarified by molecular dynamics simulations on the covalently bound Michaelis-Menten complex. A
deeper understanding of the binding properties of covalent serine hydrolase inhibitors is expected to aid
in the discovery and development of more selective covalent inhibitors.
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Introduction
The last decade has seen a renewed interest in the development of covalent inhibitors for several
classes of drug targets, including the serine hydrolase and kinase superfamily.1,2 Serine hydrolases
perform a broad array of physiological functions and have diverse substrate preferences, but they all
share a conserved catalytic nucleophilic serine residue. Serine hydrolases form a covalent acyl-enzyme
intermediate, which can be exploited by irreversible, mechanism-based inhibitors. For example, PF-
04457845 and ABX-1431 have entered clinical trials as fatty acid amide hydrolase (FAAH) and
monoacylglycerol lipase (MAGL) inhibitors for the treatment of neurological diseases, respectively.3–8
Covalent, irreversible inhibitors initially bind in a reversible fashion to the protein (i.e. the Michealis-
Menten complex) followed by a time-dependent chemical reaction that inactivates the enzyme (Figure
1A and 1B).9 The half maximum inhibitory concentration (IC50) for covalent inhibitors is dependent on
a combination of binding affinity (Ki) and reactivity (kinact). This fundamental dual aspect of covalent
inhibition is often not taken into account during the optimization of covalent irreversible inhibitors,
which is usually based on IC50 values.2,10 This may lead to the prioritization of highly reactive molecules
(large kinact) based on their high potency.11 Intrinsic high reactivity may, however, lead to a-specific
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binding to other members of the same enzyme family and unwanted adverse side effects as recently
푘푖푛푎푐푡
witnessed for BIA 10-2474.12,13 Of note, the specificity constant
is sometimes employed to guide
(
)
퐾푖
inhibitor optimization to avoid IC50-values that are assay- and time-dependent.14–16 The specificity
constant is determined by measuring the observed rate constants (kobs) using various inhibitor pre-
incubation times, but does not usually allow the independent determination and subsequent optimization
of the affinity Ki, while minimizing the reactivity kinact. Thus, alternative methods are required to
determine Ki and kinact in an independent manner.
Diacylglycerol lipases (DAGL) are serine hydrolases responsible for the synthesis of the
endocannabinoid 2-arachidonoylglycerol (2-AG).17 Modulation of DAGL activity holds therapeutic
promise for the treatment of metabolic and neuroinflammatory diseases.18–20 Several DAGL inhibitors,
including KT109, DH376 and LEI105, have been developed (Figure 1C).20–22 KT109 and DH376 belong
to the class of triazole urea inhibitors, which are capable of irreversibly binding the catalytic serine
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through the formation of a stable carbamate adduct, thereby expelling a triazole-moiety as a leaving
group (Figure 1A). This class of compounds has also shown merit as inhibitors for other serine
hydrolases, such as α/β-hydrolase domain containing protein (ABHD) 621, ABHD1123, DDHD domain-
containing protein 2 (DDHD2)24 and MAGL11,25. Structure activity studies of the DAGL (KT109 and
DH376) and MAGL (JJKK-048) inhibitors have shown that the heterocyclic leaving group is crucially
important for inhibitor activity.11,26,27 The pKa of the leaving group as determinant for the reactivity of
the urea28 was postulated to determine the activity of inhibitors.11 The exact kinetic parameters of
binding for these inhibitors have, however, thus far not been experimentally measured, thus the precise
role of the triazole heterocycle in the inhibitor activity is unknown.
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Here, we studied in detail the influence of the heterocycle in DAGL-α inhibitor DH376 on the binding
and reactivity. To this end, we synthesized a coherent set of azole derivatives of DH376 to systematically
investigate the role of the heterocycle in the activity of the inhibitor. Furthermore, we adapted a surrogate
substrate assay of DAGL-α, which allowed us to independently measure Ki and kinact of the new
inhibitors. Surprisingly, we found that the azole has a crucial role in the formation of the Michaelis-
Menten complex, rather than in modulating the reactivity. To explain this finding, Molecular Dynamics
was employed, which showed key interaction differences between compounds 1-5. Taken together, the
biological and computational data proves the importance of the heterocycle in binding affinity, not just
reactivity.
Results
To study the role of the azole heterocycle in the activity of the DAGL inhibitor DH376, a focused set of
DH376 analogues was synthesized (1-5) (Figure 1D). Four different heterocycles (1,2,3-triazole, 1,2,4-
triazole, pyrazole and imidazole) and a regio-isomer of the 1,2,3-triazole were selected, because they
span a range of five orders of magnitude in pKa.29–31 The compounds were synthesized according to
Scheme 1. The enantioselective synthetic route towards (R)-2-benzylpiperidine was adapted from Deng
et al.27 We replaced the low yielding transamination step, used to introduce an alkene at the free amine
of 10, by a simple alkylation with 4-bromobut-1-ene after nosyl protection of the amine (Scheme 1).
This protected diene was subjected to ring-closing metathesis and, after deprotection, yielded 15 in a
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three-fold higher overall yield than previously reported.27 To synthesize the leaving group azole
derivatives, a general synthetic route was devised featuring a Grignard reaction as core transformation
to yield the di-(p-fluorophenyl)methanol moiety in a single step from accessible azole esters (Scheme
1). For all but the imidazole derivative this worked without the introduction of any protecting group.
Tritylation of the imidazole ethyl ester was necessary to avoid degradation during the Grignard reaction.
Finally, the secondary amine 15 was first transformed in a carbamoyl chloride using triphosgene and
subsequently reacted with the diphenyl azoles (18, 21, 25 and 29), which furnished the inhibitors 1-5.
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Figure 1 | A) Mechanism of action of mechanism based triazole urea inhibitors for serine hydrolases. B) The
inhibition reactions for reversible and irreversible inhibition. E: enzyme, I: inhibitor, EI: Michaelis-Menten
complex of E and I, E-I: covalently bound inhibitor-enzyme complex. C) Recently published potent DAGL
inhibitors. D) Set of 5 inhibitors based on DH376 synthesized and characterized in this study.
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O
a
HO
Boc
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N
OH
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k
n
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l
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N
N
OH
OH
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N
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N
HN
O
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HN
OH
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m
o
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N
N
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OH
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OH
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OH
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p
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OH
OH
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Trt
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OH
OH
F
w
t
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v
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N
N
N
O
O
N
OH
N
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5
F
Scheme 1 | Synthesis of 1-5 implementing the optimized 9-step procedure for the synthesis of
(R)-2-benzylpiperidine 15 from commercially available N-Boc-L-phenylalanine (6), followed by the coupling to
the biphenyl-azole leaving groups synthesized using a general Grignard reaction. a) N,O-di-Me-hydroxyl-
amine∙HCl, EDCI∙HCl, DCM, 0 °C → RT, 92%; b) LiAlH4, THF, -20 °C, 96%; c) MeP(Ph)3∙Br, KHMDS, THF,
-78°C → RT, 56%; d) HCl, MeOH/H2O, quant.; e) 2-NsCl, NEt3, DMAP, DCM, 85%; f) 4-bromobut-1-ene,
K2CO3, DMF, 70 °C, 80%; g) Grubbs’ 1st gen., DCM, 40 °C, 62%; h) PhSH, NaOH, ACN/H2O, 50 °C, 99%; i)
RuCl3(H2O)3, NaBH4, DCE/MeOH, 87%; j) TMS-N3, 90 °C, 68%; k) 4-F-PhMgBr, THF, 0 °C, 94%; l) i) 15,
triphosgene, Na2CO3, DCM; ii) 18, DIPEA, DMAP, THF, 66 °C, 1.5% (1) 1.2% (2); m) MeOH, SOCl2, 65 °C,
97%; n) 4-F-PhMgBr, THF, 0 °C, 89%; o) i) 15, triphosgene, Na2CO3, DCM; ii) 21, DIPEA, DMAP, THF, 66 °C,
35%; p) KMnO4, H2O, 100 °C; q) H2SO4, EtOH, 78 °C, 47% (two steps); r) 4-F-PhMgBr, THF, 0 °C, 83%; s) i)
15, triphosgene, Na2CO3, DCM; ii) 25, DIPEA, DMAP, THF, 66 °C, 21%; t) TrCl, TEA, DCM, 0 °C → RT, 97%;
u) 4-F-PhMgBr, THF, 0 °C, 86%; v) TFA, H2O, DCM, 56%; w) i) 15, triphosgene, Na2CO3, DCM; ii) 29, DIPEA,
DMAP, THF, 66 °C, 27%.
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To determine the binding kinetics of the inhibitors we adapted the previously reported para-
nitrophenolbutyrate (PNPB) assay.32 A schematic overview of the changes made to the protocol is
depicted in Figure 2A. The principal experimental difference is that the typical pre-incubation step with
the inhibitors was omitted and enzyme activity was continuously measured from the start (t = 0). To
obtain a higher specific signal at early time points, the substrate concentration was increased to 600 µM.
Furthermore, the enzyme was pre-mixed with the assay buffer before addition to a 96-well plate, which
contained concentrated inhibitor and substrate, to minimize initial mixing effects. This yielded
reproducible substrate conversion curves (Figure 2C-E).
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Most available literature models, including the standard observed rate approximation (kobs), assume
that the enzyme concentration will not change during the incubation (Ki >> [E]).14,33–35 These models
cannot, however, be applied to potent inhibitors, such as KT109 and DH376, that will decrease the
enzyme concentration. Therefore, the kinetic model of Schwartz et al. was selected to fit to the substrate
conversion curves.10 In this model, DynaFit software is used for the numerical fitting of the full set of
differential equations governing the substrate conversion curves without making the Ki >> [E]
assumption.10,36,37 The kinetic model from Schwartz et al. was slightly adapted to incorporate the
spontaneous enzyme inactivation observed for blank measurements, where substrate depletion alone
cannot explain the decrease in substrate conversion rate. As the substrate concentration was well below
the predicted KM, the one-step substrate conversion proposed by Schwartz et al. was maintained. Initial
values for the required rate constants were derived from several preliminary experiments, and were
mostly left to be optimized by the algorithm (Figure S1).
The assay was validated using irreversible DAGL inhibitors (KT109 and DH376) and a reversible
inhibitor (LEI105) (Figure 1C). All three inhibitors were previously found to be highly active with
(sub)nanomolar potency (pIC50 8.6 to 9).20,22,38 Using seven inhibitor concentrations around their
reported IC50-values, a set of substrate conversion curves was generated. These curves were fitted with
DynaFit (Figure S1). The resulting fits and values for Ki and kinact are shown in Figure 2. As was
expected, the model does not find a fit for the kinact value for the covalent but reversible inhibitor LEI105.
The found Ki-values (all between 0.2 and 0.4 nM) were generally in line with the high potency described
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in literature, although LEI105 was somewhat more active than previously reported.22 The inactivation
rates for KT-109 and DH376 were similar (kinact = ± 0.07 min-1).
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Figure 2 | Schematic overview of previously published PNP-butyrate based surrogate substrate assay (A) and the
adapted workflow to determine binding kinetics (B). Kinetics of binding of KT109 (C), DH376 (D) and LEI105
(E), data fits are summarized in (F). For clarity not all substrate conversion curves used for the curve fitting are
shown. Markers denote measured absorbance, lines denote fitted model.
Next, we tested inhibitors 1-5 to determine the influence of the leaving group on their potency in the
standard surrogate substrate assay. A large range in IC50-values was observed (Figure 3A, Table 1). Both
regioisomers 1 and 2 were low nanomolar inhibitors, whereas the 1,2,4-triazole (3) had a reduced
potency (IC50 = 3.4 µM) and the imidazole (5) was inactive (IC50 > 10 µM). Pyrazole (4) had an
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intermediate potency with IC50 of 0.21 µM. The IC50-values were used to guide the selection of inhibitor
concentrations for the kinetic assay (Figure 3B, Table 1). For all but the imidazole compound 5 we were
able to determine the kinetic parameters. Intriguingly, the inactivation rates for 1 and 2 (kinact = 0.22 and
0.32 min-1, respectively), were 2-3 times higher than for KT109 and DH376, but they had a lower
binding affinity (Ki = 10 and 339 nM, respectively). Unexpectedly, the inactivation rates for 3 and 4
were comparable to DH376 and KT109, whereas there is 10,000-fold difference in pKa between these
heterocycles (Table 1). Yet, the binding affinity of 3 and 4 was substantially reduced (Ki > 10 µM),
thereby explaining their higher IC50-values.
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Figure 3 | pIC50 determination of compounds 1-5 (A) and kinetic fits (B). All data points are measured as n = 4,
positive controls (DMSO) as n = 8. Markers denote mean values, error bars denote the SEM, lines are fitted data
models.
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Table 1 | Potency and kinetic parameters of the focused set of DH376 derivatives 1-5.
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Compound
pIC50
Ki (nM)
10.4 ± 2.0
339 ± 55
kinact (min-1)
0.22 ± 0.03
0.32 ± 0.04
0.075 ± 0.005
0.080 ± 0.005
N.D.
pKa
1
2
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4
5
8.52 ± 0.27
8.42 ± 0.28
5.47 ± 0.07
6.68 ± 0.41
< 4.5
9.331
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9.331
13770 ± 910
10800 ± 910
N.D.
10.029
14.230
14.430
To understand the reasons behind this difference in binding, in silico experiments were carried out.
In a two-step process, firstly covalent docking of compounds 1- 5 to Ser472 of a previously developed
homology model32 was performed (Figure 4, Figure S3). Subsequently dynamic evolution of the protein-
ligands interactions was followed using molecular dynamics for all complexes (Figures S3-7). The
docked poses are assumed to reflect the Michaelis-Menten intermediate of the reaction displayed in
Figure 1A. All complexes remained stable over the trajectories and the negatively charged oxygen was
continuously stabilized by the backbone of both Thr400 and Leu473 (Figures S4, S5 and S6).
Assessment of the interactions through the frames of the dynamic evolution allowed the deconvolution
of the observed binding behaviour.
The observed high potency of 1 and 2 could be explained by the major hydrogen bonding with His650
(Figure 4A), similar as has been previously shown for α-positioned heterocycles for related serine
hydrolases like FAAH and others.39,40 The 1,2,3-triazoles are able to form this bond through the nitrogen
in position 3. His650 is part of the catalytic triad and has been postulated to bind in this manner before,
based on the covalent docking of α-ketoheterocycles in a homology model of DAGL-α.41 Additionally
compound 1 forms a strong π-stacking interaction with His471 and a stable hydrogen bonding
interaction with Tyr303, explaining the difference in potency observed with 2, which forms a π-stacking
interaction with His650, and less stable hydrogen bonding interaction with the nitrogen in position 1
and His471 (Supplementary Figure 3). Compound 4 is also able to make this very stable hydrogen
bonding between the nitrogen in position 2 and His650, potentially explaining the intermediate potency.
Additionally, the hydroxyl interacts through a water-bridge with His471.
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Interestingly, the 1,2,4-triazole and imidazole rings-containing compounds (3 and 5) interact mostly
only weakly through water bridging with His650. In many frames these azoles are observed to rotate to
a 90-degree angle which causes the loss of this interaction with His650. The further difference between
the potencies of both these compounds may be explained by the capacity of nitrogen in position 2 in 3
to form water bridges with Tyr653 or Ser185 when adopting this 90-degree angle, which is not possible
for the imidazole nitrogen in 5.
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Figure 4 | Representative frames of the molecular dynamics simulations showing highly potent 1,2,3-triazole 1
(A) and inactive imidazole 5 (B) bound to the DAGL-α homology model. Predominant interactions are shown,
annotated with the percentage of frames showing this interaction (3 separate simulations, 100 frames each).
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Discussion and Conclusions
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We developed a surrogate substrate based assay to determine the kinetic parameters of binding and
reactivity of triazole urea inhibitors of the serine hydrolase DAGL-α. Having the ability to discern the
kinetics of binding should enable the optimization of the affinity of the inhibitors for the enzyme, the
Ki, while controlling the reactivity kinact, to minimize the off-target reactivity. The assay was validated
using three well-characterized published DAGL inhibitors. Five DH376 derivatives were synthesized to
study the role of the leaving group in the affinity and reactivity with DAGL-α. The IC50-values correlated
with the Ki and kinact with an R2 of 0.73 and 0.77, respectively (Figure 5A, B). The main reason for the
large differences observed in IC50-values for the five inhibitors was the strong reduction in binding
affinity for the pyrazole and 1,2,4-triazole compounds compared to the 1,2,3-triazole inhibitors. In
agreement with the known SAR27, 1 has a lower pIC50 than DH376. This is shown to be primarily due
to a decrease in affinity, which signifies the role of the propargylether in DH376. The kinact of DH376
was found to be slightly lower than 1. No obvious explanation for this finding presents itself, but one
could speculate the ether-oxygen to interfere in the hydrogen bonding network needed for
hydrolysis.Unexpectedly, it was shown that the 1,2,4-triazole 3 and pyrazole 4 inhibitors were as
reactive as DH376 and KT109, which is in stark contrast to the five orders of magnitude difference in
pKa. This showed that the leaving group acidity does not correlate with the rate of inactivation kinact
(Figure 5C).
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Figure 5 | pIC50 correlates with both pKi (A) and kinact (B) but pKa (C) does not correlate with reactivity for the
inhibitors 1-4. Dotted lines denote 90% confidence interval.
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The striking difference in binding affinity was further explored using molecular dynamics.
Compounds 1-5 were assumed to bind covalently to the catalytic serine upon Michaelis-Menten
complex formation. The tetrahedral intermediate was evolved using molecular dynamics to analyze the
interactions with the enzyme. The MD simulations also showed a large influence of the positioning and
number of nitrogens in the ring, agreeing with the observations made in the kinetics assay. However,
while these simulations are crucial for an understanding of the experimental data, the MD could not be
used to study the reaction progress or (relative) speeds of the final covalent modification.
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The assay presented here, in combination with the data analysis through numerical fitting, could be
translated to work on a multitude of serine hydrolases. As long as a sensitive and robust (surrogate)
substrate assay is available that can be interrogated in a time-dependent manner it should in principle be
possible to derive structure kinetics relationships. These relationships provide important insights into
the mode of action and can aid in the optimization of covalent serine hydrolase inhibitors in an affinity
directed manner. For the DAG lipase inhibitors, this may lead to more selective inhibitors more suitable
for further in vivo target validation studies.
To conclude, we have developed a kinetic assay to study the influence of the heterocyclic core of
triazole ureas as covalent, mechanism-based inhibitors of diacylglycerol lipase-α. We found that the pKa
of the leaving group did not correlate with the reactivity of the inhibitors, but that the position of the
nitrogen atom in the heterocycle is of importance in its binding affinity. These findings were in
agreement with molecular dynamics simulations on covalently docked inhibitors in a homology model
of DAGL-α. Detailed knowledge of structure kinetic relationships is expected to guide the optimization
of more selective and well-balanced irreversible inhibitors of serine hydrolases.
Experimental Section
Chemical biology methods
Cell culture and membrane preparation
HEK293T cells were grown in DMEM with stable glutamine and phenolred (PAA) with 10% New Born Calf serum,
penicillin and streptomycin. Cells were passaged every 2-3 days by resuspending in medium and seeding them to
appropriate confluence. Membranes were prepared from transiently transfected HEK293T cells. One day prior to
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transfection 107 cells were seeded in a 15 cm petri dish. Cells were transfected by the addition of a 3:1 mixture of
polyethyleneimine (60 µg) and plasmid DNA (20 µg) in 2 mL serum free medium. The medium was refreshed after 24
hours, and after 72 h the cells were harvested by suspending them in 20 mL medium. The suspension was centrifuged
for 10 min at 1000 g, and the supernatant was removed. The cell pellet was stored at -80 °C until use.
Cell pellets were thawed on ice and suspended in lysis buffer (20 mM Hepes, 2 mM DTT, 0.25 M sucrose, 1 mM MgCl2,
25 U/mL benzonase). The suspension was homogenized by polytrone (3x 7 sec) and incubated for 30 min on ice. The
suspension was subjected to ultracentrifugation (93,000 g, 30 min, 4 °C, Beckman Coulter, Type Ti70 rotor) to yield the
cytosolic fraction in the supernatant and the membrane fraction as a pellet. The pellet was resuspended in storage buffer
(20 mM Hepes, 2 mM DTT). The protein concentration was determined with Quick Start Bradford assay (Biorad). The
protein fractions were diluted to a total protein concentration of 1 mg/mL and stored in small aliquots at -80 °C until
use.
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Surrogate substrate assay
The biochemical mDAGL-α activity assay is based on the method previously described.32 100 μL reactions were
performed in flat bottom Greiner 96-wells plates in a 50 mM pH 7.2 Hepes buffer. Membrane protein fractions from
HEK293T cells transiently transfected with mDAGL-α (0.05 μg/μL final concentration) were used as mDAGL-α source.
Inhibitors were introduced in 2.5 μL DMSO. The mixtures were incubated for 20 minutes before 5.0 μL 6 mM PNP-
butyrate (final concentration 0.3 mM) in 50% DMSO was added (final DMSO concentration 5.0%). Reactions were
allowed to progress for 30 minutes at 20 °C before OD (420 nm) was measured using a TECAN GENios plate reader.
All experiments were performed at N=2, n=2 for experimental measurements and N=2, n=4 for controls.
Data analysis: Z’-factor of each plate was determined for the validation of each experiment, using the following formula
Z’=1-3(σpc+ σnc)/(µpc - µnc). The OD from the positive control (pc: DAGL DMSO), and the negative control (nc: 10 µM
THL) was used. Plates were accepted for further analysis when Z’>0.6. Measurements were corrected for the average
absorption of the negative control (10 µM THL). The average, standard deviation (SD) and standard error of mean
(SEM) were calculated and normalized to the corrected positive control. Data was exported to Graphpad Prism 7.0 for
the calculation of the pIC50 using a non-linear dose-response analysis.
DynaFit setup
DynaFit version 4 was used with an academic license. For batch processing the command line interface was used. The
raw data were pre-processed using Microsoft Excel 2016 and exported to tab delimited text files for use with DynaFit.
Scripts were generated manually or using a purpose-made python script. An example DynaFit script is shown in Figure
S1.
The contents of the header [task] follow directly from the DynaFit manual and simply state that the program should fit
progress curves using the data supplied.
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The section [mechanism] was built based on standard enzyme kinetics. The simplified hit and run
(E + S ---> E + P) was used for the substrate conversion as the KM of the surrogate substrate is too high to be
determined reliably experimentally.10,32 The additional enzyme degradation step (E ---> E*) was included as the
progress rate curves for the DMSO blanks decreased more than could be explained by the reduction in substrate
concentration (which is accounted for in the set of differential equations fitted).
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The rate constants defined in [constants] were set empirically but are all left to be optimized. The exception is kon, which
is fixed to 100,000 µM-1∙min-1, but the variable itself is dependent on koff (and vice versa), so only the ratio of the two
(Ki) is physically meaningful in this experimental setup.
As the enzyme is obtained by overexpression in HEK293T cells the exact concentration is unknown. Data from the
previously published PNPB-based assay used for pIC50 determination indicate that the assay limit lies around 9, which
puts the enzyme concentration at ± 1 nM. It is left to be optimised by DynaFit.
The value for P given in the [responses] section is essentially the absorption coefficient of the converted surrogate
substrate in AU∙µM-1, which was determined experimentally (Figure S2).
Molecular Dynamics
Ligand Preparation
Molecular structures of compounds 1 to 5 drawn with the specified chirality and prepared for docking using LigPrep42
from Schrödinger. Default LigPrep settings were applied, using Epik43 for the generation of ionization states of
heteroatoms at pH = 7.0 ± 2.0 and the OPLS3e force-field44 for geometry optimization. No tautomers were generated by
the program resulting in one standardized structure per ligand.
Protein preparation
A previously described homology model of DAGL-α32 based on template with PDB code 1GT6 was prepared for docking
using the Protein Preparation protocol from the Schrödinger 2018-4 suite with default settings. Ionization states of
heteroatoms were generated with Epik at pH 7.0 ± 2.0 resulting in the protonation of the imidazole ring of His471 and
His650.
Covalent docking
Covalent docking of the prepared compounds to Ser 472 was performed using the Schrödinger 2018-3 suite45 with
standard settings, generating one pose per compound. Docked ligands were confined to the enclosing box defined by the
following residues: Tyr303, Gly399, Thr400, Thr408, Asp409, Met432, His471, Ser472, Leu473, Leu647, His650,
Leu651 and Gly658.
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Each protein-ligand complex was then subjected to molecular dynamics using Desmond Molecular Dynamics System
from Schrödinger46. The system was set up using default settings, water solvent model SPC47 and OPLS3 forcefield44.
Simulations were performed in triplicates at 300 K and 1.01 bar using hydrogen mass repartitioning with a runtime of
300 ns per run.
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Chemistry
General remarks
All reactions were performed using oven- or flame-dried glassware and dry (molecular sieves) solvents. Reagents were
purchased from Alfa Aesar, Sigma-Aldrich, Acros, and Merck and used without further purification unless noted
otherwise. All moisture sensitive reactions were performed under an argon or nitrogen atmosphere.
1H and 13C NMR spectra were recorded on a Bruker DPX-300 (300 MHz), AV-400 (400 MHz) or DRX-500 (500 MHz).
Used software for interpretation of NMR-data was Bruker TopSpin 1.3 and MestreNova 11.0. Chemical shift values are
reported in ppm with tetramethylsilane or solvent resonance as the internal standard (CDCl3: δ 7.26 for 1H, δ 77.16 for
13C; ACN-d3: δ 1.94 for H, δ 1.32 for 13C; MeOD: δ 3.31 for H, δ 49.00 for 13C).48 Data are reported as follows:
chemical shifts (δ), multiplicity (s = singlet, d = doublet, dd = double doublet, td = triple doublet, t = triplet, q = quartet,
bs = broad singlet, m = multiplet), coupling constants J (Hz), and integration.
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Liquid chromatography was performed on a Finnigan Surveyor LC/MS system, equipped with a C18 column. Final
compound purity was ≥95% as determined by LC/MS, analytical traces are included in Supplementary Information.
Flash chromatography was performed using SiliCycle silica gel type SiliaFlash P60 (230−400 mesh). TLC analysis was
performed on Merck silica gel 60/Kieselguhr F254, 0.25 mm. Compounds were visualized using KMnO4 stain (K2CO3
(40 g), KMnO4 (6 g), and water (600 mL)) or CAM stain (Ce(NH4)4(SO4)4∙2H2O (ceric ammonium sulfate: 10 g);
ammonium molybdate (25 g); conc. H2SO4 (100 mL); H2O (900 mL)). Preparative HPLC (Waters, 515 HPLC pump M;
Waters, 515 HPLC pump L; Waters, 2767 sample manager; Waters SFO System Fluidics Organizer; Waters Acquity
Ultra Performance LC, SQ Detector; Waters Binary Gradient Module) was performed on a Waters XBridgeTM column
(5 μM C18, 150 x 19 mm). Diode detection was done between 210 and 600 nm. Gradient: ACN in (H2O + 0.2% TFA).
Chiral HPLC analysis was performed after benzoylation of the free amine on a Daicel Chiralpak AD column (250 x 4.5
mm, 10 μm particle size) using 10 % isopropyl alcohol in hexane as eluent (1.0 mL/min, UV-detection at 254 nm) Rt=
15.1 min (R-enantiomer 12.8 min). High resolution mass spectra (HRMS) were recorded by direct injection on a q-TOF
mass spectrometer (Synapt G2-Si) equipped with an electrospray ion source in positive mode with Leu-enkephalin (m/z
= 556.2771) as an internal lock mass. The instrument was calibrated prior to measurement using the MS/MS spectrum
of Glu-1-fibrinopeptide B.
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General procedure 1: triphosgene coupling of 2-benzylpiperidine and bis(4-fluorophenyl) heterocycle
Triphosgene (0.7 eq.) was dissolved in dry DCM (0.1 M) and to this solution 2-benzylpiperidine (1 eq.) and Na2CO3 (1
eq.) were added at 0 °C. The mixture was stirred for 1 hour, warming to RT. The mixture was then filtered and
concentrated in vacuo. The residue was taken up in dry THF, followed by addition of a bis(4-fluoro-phenyl)heterocycle
(1 eq.), DMAP (0.1 eq.) and DIPEA (1.1 eq.). The reaction mixture was refluxed to completion. The reaction was
quenched with saturated NH4Cl (aq.), after which the water layer was extracted three times with EtOAc. The combined
organic layers were washed with brine, dried with MgSO4, filtered and concentrated under reduced pressure.
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(R)-(2-Benzylpiperidin-1-yl)(4-(bis(4-fluorophenyl)(hydroxy)methyl)-2H-1,2,3-triazol-2-yl)methanone (1)
and (R)-(2-benzylpiperidin-1-yl)(4-(bis(4-fluorophenyl)(hydroxy)methyl)-1H-1,2,3-triazol-1-yl)methanone
(2)
Synthesized according to General Procedure 1 from 18 (123 mg, 0.428 mmol). The N1-isomer was isolated as first
eluting isomer (1.63 mg, 3.3 µmol, 1.2%). 1H NMR (400 MHz, CDCl3) δ 7.41 – 6.57 (m, 14H), 4.76 (s, 1H), 4.40 – 4.18
(m, 1H), 3.56 (d, J = 66.9 Hz, 1H), 3.41 – 2.81 (m, 2H), 2.65 (s, 1H), 2.08 – 1.39 (m, 6H). Purity of >95% as determined
by LC/MS (Supplementary Information). HRMS: Calculated for [C28H26F2N4O2+H]+ = 488.2079, found = 488.2090.
N2-isomer (2.14 mg, 4.4 µmol, 1.5%): 1H NMR (400 MHz, CDCl3) δ 7.48 (s, 1H), 7.40 – 6.70 (m, 13H), 5.04 – 3.66
(m, 2H), 3.47 (s, 1H), 3.26 (t, J = 13.3 Hz, 1H), 3.16 – 2.81 (m, 2H), 1.94 – 1.43 (m, 6H). Purity of ≥95% as determined
by LC/MS. HRMS: Calculated for [C28H26F2N4O2+H]+ = 488.2079, found = 488.2091.
(R)-(2-Benzylpiperidin-1-yl)(3-(bis(4-fluorophenyl)(hydroxy)methyl)-1H-1,2,4-triazol-1-yl)methanone (3)
Synthesized according to General Procedure 1 from 21 (65 mg, 0.23 mmol). The title compound was obtained as a white
solid (34.7 mg, 0.071 mmol, 35%). 1H NMR (400 MHz, CD3CN) δ 8.04 (bs, 1H), 7.35 (d, J = 6.6 Hz, 4H), 7.12 (s, 3H),
7.07 – 6.70 (m, 7H), 4.88 (s, 1H), 4.72 (s, 1H), 4.03 (d, J = 15.5 Hz, 1H), 3.23 (t, J = 13.1 Hz, 1H), 2.70 (s, 1H), 1.83 –
1.32 (m, 6H). Purity of ≥95% as determined by LC/MS. HRMS: Calculated for [C28H26F2N4O2+H]+ = 488.2097, found
= 488.2096.
(R)-(2-Benzylpiperidin-1-yl)(3-(bis(4-fluorophenyl)(hydroxy)methyl)-1H-pyrazol-1-yl)methanone (4)
Synthesized according to General Procedure 1 from 25 (65 mg, 0.23 mmol). The title compound was obtained as a white
solid (21 mg, 0.043 mmol, 21%). 1H NMR (400 MHz, CD3CN) δ 7.66 – 7.49 (m, 1H), 7.42 – 7.29 (m, 4H), 7.17 (dd, J
= 5.1, 1.9 Hz, 3H), 7.13 – 6.92 (m, 6H), 6.22 (d, J = 2.6 Hz, 1H), 4.77 (s, 1H), 4.59 (s, 1H), 4.17 – 3.99 (m, 1H), 3.25
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(td, J = 13.4, 3.0 Hz, 1H), 3.10 (dd, J = 13.5, 9.0 Hz, 1H), 2.83 – 2.68 (m, 1H), 1.88 – 1.21 (m, 6H). Purity of ≥95% as
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determined by LC/MS. HRMS: Calculated for [C29H27F2N3O2+H]+ = 488.2144, found = 488.2140.
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(R)-(2-Benzylpiperidin-1-yl)(4-(bis(4-fluorophenyl)(hydroxy)methyl)-1H-imidazol-1-yl)methanone (5)
Synthesized according to General Procedure 1 from 29 (83 mg, 0.29 mmol). The title compound was obtained as a white
solid (38 mg, 0.078 mmol, 27%). 1H NMR (400 MHz, CD3CN) δ 7.42 (s, 1H), 7.38 – 6.99 (m, 13H), 6.27 (s, 1H), 4.47
(s, 1H), 4.30 (qt, J = 7.1, 3.8 Hz, 1H), 3.81 (d, J = 13.7 Hz, 1H), 3.32 (td, J = 13.3, 2.9 Hz, 1H), 3.19 (dd, J = 13.7, 10.0
Hz, 1H), 2.78 (dd, J = 13.7, 5.5 Hz, 1H), 1.92 – 1.63 (m, 6H). Purity of ≥95% as determined by LC/MS. HRMS:
Calculated for [C29H27F2N3O2+H]+ = 488.2144, found = 488.2142.
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tert-Butyl (S)-(1-(methoxy(methyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamic acid (7)
N-Boc-L-phenylalanine 6 (24.16 g, 91 mmol), N,O-dimethylhydroxylamine hydrochloride (9.95 g, 102 mmol) and 4-
methylmorpholine (11.25 mL, 102 mmol) were dissolved in dichloromethane and cooled to 0 °C. EDCI-HCl (18.75 g,
98 mmol) was added in three portions with a 15 min interval. After consumption of the starting material, the reaction
mixture was washed with sat. aq. NH4Cl, sat. aq. NaHCO3 and brine. The organic phase was dried (MgSO4), filtered and
concentrated under reduced pressure to obtain the pure title compound as a honey like oil (25.9 g, 84 mmol, 92%).1H
NMR (400 MHz, CDCl3) δ 7.36 – 7.06 (m, 6H), 5.04 – 4.85 (m, 1H), 3.65 (s, 3H), 3.17 (s, 3H), 3.09 – 2.96 (m, 1H),
2.94 – 2.80 (m, 1H), 1.37 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 155.27, 136.70, 129.56, 128.45, 126.86, 79.67, 61.65,
51.62, 43.93, 38.97, 28.42.
tert-Butyl (S)-(1-oxo-3-phenylpropan-2-yl)carbamate (8)
7 (25.9 g, 84 mmol) was dissolved in THF and cooled to -15 °C. Subsequently a 1 M solution of LiAlH4 in THF (42 mL,
42 mmol) was added slowly. Upon completion, the reaction was quenched with 25% aq. KHSO4, allowed to warm up
to RT and stirred vigorously. Ethyl acetate was added, and the organic phase was separated, washed with sat. aq. NaHCO3
and brine, dried (MgSO4), filtered and concentrated under reduced pressure to give the title compound as a white solid.
(20.2 g, 81 mmol, 96%). 1H NMR (400 MHz, CDCl3) δ 9.63 (s, 1H), 7.43 – 7.04 (m, 5H), 5.18 – 4.99 (m, 1H), 4.43 (q,
J = 6.8 Hz, 1H), 3.12 (d, J = 6.7 Hz, 2H), 1.41 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 199.56, 135.90, 129.46, 128.88,
127.19, 80.33, 60.91, 35.58, 28.39.
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tert-Butyl (S)-(1-phenylbut-3-en-2-yl)carbamate (9)
To solution of potassium bis(trimethylsilyl)amide (27 g, 135 mmol) in dry THF was added
a
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methyltriphenylphosphonium bromide (54.8 g, 153 mmol). The resulting mixture was stirred for 3 hr and subsequently
cooled to -78 °C, after which a solution of 8 (22.5 g, 90 mmol) in THF was added. The reaction was allowed to warm
up to RT overnight and quenched with sat. aq. NH4Cl. EtOAc was added and the organic phase was separated, washed
with sat. aq. NaHCO3 and brine, dried (MgSO4), filtered and concentrated under reduced pressure. The residue was
purified with silica chromatography (8% ethyl acetate in petroleum ether) to give the desired product as a white, waxy
solid (12.6 g, 50.9 mmol, 56%). 1H NMR (400 MHz, CDCl3) δ 7.34 – 7.13 (m, 5H), 5.88 – 5.71 (m, 1H), 5.16 – 5.03
(m, 2H), 4.45 (d, J = 27.0 Hz, 2H), 2.83 (d, J = 6.5 Hz, 2H), 1.40 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 155.33, 138.18,
137.53, 129.68, 128.44, 126.59, 114.84, 79.53, 53.58, 41.60, 28.47.
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(S)-1-Phenylbut-3-en-2-amine (10)
9 (9.7 g, 39.2 mmol) was dissolved in absolute methanol and 4 M aq. HCl was added. After TLC showed full
consumption of the starting material, the mixture was concentrated under reduced pressure and diluted with water. The
solution was washed with diethyl ether and aq. NaOH was used to make the aqueous layer basic (pH > 12). The aqueous
phase was extracted 3x with chloroform. The organic layers were combined, dried (MgSO4), filtered and concentrated
under reduced pressure to give the title compound in quantitative yield. Epimerised product that was formed during
Wittig olefination was removed by recrystallization form toluene/n-propyl alcohol with N-acetyl-L-leucine according to
literature procedure,49 yielding the amine as a yellow oil with an enantiomeric ratio of 97:3 as determined by chiral
HPLC (vide infra). 1H NMR (400 MHz, CDCl3) δ 7.36 – 7.12 (m, 5H), 5.89 (ddd, J = 16.8, 10.3, 6.2 Hz, 1H), 5.14 (dt,
J = 17.2, 1.5 Hz, 1H), 5.04 (dt, J = 10.3, 1.4 Hz, 1H), 3.64 – 3.52 (m, 1H), 2.83 (dd, J = 13.3, 5.4 Hz, 1H), 2.62 (dd, J =
13.3, 8.3 Hz, 1H), 1.31 (s, 3H). 13C NMR (101 MHz, CDCl3) δ 142.49, 138.86, 129.51, 128.50, 126.45, 113.77, 55.57,
44.43.
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(S)-2-Nitro-N-(1-phenylbut-3-en-2-yl)benzenesulfonamide (11)
10 (3.5 g, 23.8 mmol), triethylamine (4.88 mL, 35.7 mmol), N,N-dimethylaminopyridine (1.45 g, 11.9 mmol) and 2-
nitrobenzenesulphonyl chloride (6.85 g, 30.9 mmol) were dissolved in dry DCM and stirred overnight, after which the
reaction mixture was concentrated under reduced pressure. Flash column chromatography (20% ethyl acetate in
petroleum ether) yielded the desired product with trace impurities as an orange oil (6.7 g, 20 mmol, 85%). 1H NMR (400
MHz, CDCl3) δ 8.01 – 7.90 (m, 1H), 7.83 – 7.71 (m, 1H), 7.69 – 7.58 (m, 2H), 7.18 – 7.01 (m, 5H), 5.81 – 5.64 (m, 1H),
5.40 (d, J = 7.9 Hz, 1H), 5.13 (dt, J = 17.1, 1.2 Hz, 1H), 5.03 (dt, J = 10.3, 1.1 Hz, 1H), 4.32 – 4.17 (m, 1H), 2.92 (dd, J
= 13.8, 6.1 Hz, 1H), 2.79 (dd, J = 13.8, 7.8 Hz, 1H). 13C NMR (101 MHz, CDCl3) δ 137.21, 136.22, 134.84, 133.22,
132.92, 130.79, 129.46, 128.54, 127.03, 125.53, 116.57, 58.68, 42.16.
(S)-N-(But-3-en-1-yl)-2-nitro-N-(1-phenylbut-3-en-2-yl)benzenesulfonamide (12)
11 (6.7g, 20.2 mmol) was dissolved in DMF and K2CO3 (11.1 g, 81 mmol) and 4-bromo-1-butene (2.46 mL, 24.2 mmol)
were added. The mixture was heated to 70 °C and stirred vigorously. After 24 hr, an extra portion of 4-bromo-1-butene
(2.46 mL, 24.2 mmol) was added and the resulting mixture was stirred for 72 h. The reaction was allowed to cool down
to RT, diluted with brine and extracted 3x with EtOAc. Combination, drying (MgSO4), filtration and concentration of
the organic phases yielded the desired product as a brown oil (6.24 g, 16.2 mmol, 80%). 1H NMR (400 MHz, CDCl3) δ
7.92 – 7.84 (m, 1H), 7.69 – 7.52 (m, 3H), 7.25 – 7.12 (m, 5H), 5.89 – 5.64 (m, 2H), 5.17 – 5.02 (m, 4H), 4.72 – 4.62 (m,
1H), 3.50 – 3.31 (m, 2H), 3.08 (dd, J = 13.5, 5.9 Hz, 1H), 2.95 (dd, J = 13.5, 9.2 Hz, 1H), 2.50 – 2.31 (m, 2H). 13C NMR
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(S)-6-Benzyl-1-((2-nitrophenyl)sulfonyl)-1,2,3,6-tetrahydropyridine (13)
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A solution of 12 (6.24 g, 16.2 mmol) in DCM was purged with argon and 1st generation Grubbs catalyst (400 mg, 3
mol%) was added. The mixture was heated to 40 °C and stirred overnight. Volatiles were removed under reduced
pressure and flash column chromatography (40% diethyl ether in petroleum ether) yielded the desired product as brown
powder (3.57 g, 9.96 mmol, 62%). 1H NMR (400 MHz, CDCl3) δ 7.85 (d, J = 7.7 Hz, 1H), 7.69 – 7.48 (m, 3H), 7.25 –
7.09 (m, 5H), 5.87 – 5.74 (m, 1H), 5.62 (d, J = 10.6 Hz, 1H), 4.56 (s, 1H), 3.93 (dd, J = 14.4, 6.2 Hz, 1H), 3.15 (ddd, J
= 15.2, 11.7, 4.1 Hz, 1H), 3.00 (dd, J = 13.1, 6.0 Hz, 1H), 2.89 (dd, J = 13.1, 8.3 Hz, 1H), 2.21 – 2.04 (m, 1H), 1.93 (dt,
J = 18.1, 5.0 Hz, 1H). 13C NMR (101 MHz, CDCl3) δ 137.28, 134.48, 133.30, 131.84, 130.44, 129.69, 128.50, 127.27,
126.79, 125.61, 124.27, 55.78, 41.71, 39.11, 24.33.
(S)-6-Benzyl-1,2,3,6-tetrahydropyridine (14)
To a solution of thiophenol (2.56 mL, 24.9 mmol) in acetonitrile cooled with ice was added a 2 M aq. solution of NaOH
(12.45 mL, 24.9 mmol). After stirring for 10 minutes, the ice bath was removed and a solution of 13 (3.57 g, 9.96 mmol)
in acetonitrile was added slowly. The resulting mixture was heated to 50 °C. When TLC showed full conversion of the
starting material, the reaction was cooled to RT and diluted with aq. HCl so that the pH was below 2. The aqueous layer
was washed with Et2O and diluted with aq. NaOH until the pH was above 12. It was then extracted 3x with ethyl acetate.
The organic layers were combined, dried (MgSO4), filtered and concentrated to afford the desired product as yellow oil
(1.71 g, 9.86 mmol, 99%). 1H NMR (400 MHz, CDCl3) δ 7.37 – 7.15 (m, 5H), 5.84 – 5.75 (m, 1H), 5.64 (dq, J = 10.1,
2.0 Hz, 1H), 3.61 – 3.51 (m, 1H), 3.17 – 2.99 (m, 1H), 2.85 – 2.75 (m, 2H), 2.70 (dd, J = 13.2, 8.8 Hz, 1H), 2.26 – 2.12
(m, 1H), 2.02 – 1.91 (m, 1H). 13C NMR (101 MHz, CDCl3) δ 138.97, 130.25, 129.39, 128.57, 126.43, 126.22, 55.47,
42.56, 42.12, 25.86.
(R)-2-Benzylpiperidine (15)
In a three-neck flask containing two stoppers and one septum with empty balloons, 14 (1.70 g, 9.81 mmol) was dissolved
in dichloroethane/methanol 10:3. This solution was purged with argon and cooled to 0 °C, after which RuCl3(H2O)3 (257
mg, 0.98 mmol) was added. NaBH4 (1.86 g, 49 mmol) was added quickly while capturing the formed H2 gas in the empty
balloons, thus keeping the reaction under hydrogen atmosphere. The reaction was allowed to warm up to RT and stirred
overnight. Aqueous HCl was then added, so that the water layer had a pH of below 2. The aqueous layer was washed
with Et2O and diluted with aq. NaOH until the pH was above 12. The water layer was extracted thrice with ethyl acetate.
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The organic layers were combined, dried (MgSO4), filtered and concentrated to yield the title compound as a yellow
waxy solid (1.5 g, 8.6 mmol, 87%). 1H NMR (400 MHz, CDCl3) δ 7.38 – 7.03 (m, 5H), 3.08 – 2.89 (m, 1H), 2.77 – 2.64
(m, 2H), 2.64 – 2.46 (m, 2H), 1.84 – 1.73 (m, 1H), 1.73 – 1.63 (m, 1H), 1.63 – 1.52 (m, 1H), 1.52 – 1.38 (m, 1H), 1.37
– 1.15 (m, 3H). 13C NMR (101 MHz, CDCl3) δ 139.12, 129.23, 128.39, 126.20, 58.26, 47.08, 43.81, 32.77, 26.08, 24.80.
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Methyl 1H-1,2,3-triazole-4-carboxylate (17)
This protocol was based on literature procedure.50 A mixture of azidotrimethylsilane (2.6 mL, 20 mmol) and methyl
propiolate 16 (1.8 mL, 20 mmol) was heated for 4 h at 90 °C, concentrated and coevaporated with MeOH to yield the
title compound as a white solid (1.74 g, 14 mmol, 68%). 1H NMR (400 MHz, MeOD) δ 8.35 (s, 1H), 3.92 (s, 3H). 13
NMR (101 MHz, MeOD) δ 162.61, 139.63, 131.92, 52.53.
C
Bis(4-fluorophenyl)(1H-1,2,3-triazol-4-yl)methanol (18)
17 (100 mg, 0.787 mmol) was dissolved in THF and cooled to 0 °C. Under vigorous stirring, a 2M solution of 4-
fluorophenylmagnesium bromide in Et2O (1.38 mL, 2.75 mmol) was added dropwise. The reaction mixture was allowed
to warm up to RT and stirred overnight. The reaction was quenched with sat. aq. NH4Cl. The aqueous phase was extracted
with DCM (3x). The combined organic layers were dried (MgSO4), filtered and concentrated under reduced pressure.
The residue was purified using flash column chromatography (40% to 60% ethyl acetate in pentane) in order to obtain
the title compound as a white solid (210 mg, 0.731 mmol, 94%). 1H NMR (400 MHz, MeOD) δ 7.60 (s, 1H), 7.45 – 7.33
(m, 4H), 7.15 – 6.98 (m, 4H).
Methyl 1H-1,2,4-triazole-3-carboxylate (20)
1H-1,2,4-triazole-3-carboxylic acid 19 (250 mg, 2.21 mmol) was dissolved in MeOH (50 mL) and cooled to 0 °C.
Thionyl chloride (0.48 ml, 6.6 mmol) was slowly added to the solution. The mixture was then heated to reflux for 3 h
after which it was cooled to RT and concentrated in vacuo to yield the title compound (271 mg, 2.14 mmol, 97%) as a
white solid. 1H NMR (400 MHz, MeOD) δ 9.24 (s, 1H), 4.05 (s, 3H).
Bis(4-fluorophenyl)(1H-1,2,4-triazol-3-yl)methanol (21)
20 (100 mg, 0.787 mmol) was dissolved in THF and cooled to 0 °C. Under vigorous stirring, a 2 M solution of 4-
fluorophenylmagnesium bromide in Et2O (1.37 mL, 2.75 mmol) was added dropwise. The reaction mixture was allowed
to warm up to RT and stirred overnight. The reaction was quenched with sat. aq. NH4Cl. The aqueous phase was extracted
with ethyl acetate (3x). The combined organic layers were dried (MgSO4), filtered and concentrated under reduced
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pressure, yielding the title compound as an off-white solid (201 mg, 0.700 mmol, 89%). 1H NMR (400 MHz, CD3CN)
δ 8.21 (s, 1H), 7.40 (dd, J = 8.7, 5.4 Hz, 4H), 7.08 (t, J = 8.7 Hz, 4H). 13C NMR (101 MHz, MeOD) δ 163.23, 160.78,
140.15, 133.42, 128.89 (d, J = 8.2 Hz), 115.17, 114.42 (d, J = 21.7 Hz), 76.63.
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1H-Pyrazole-3-carboxylic acid (23)
Synthesis based on published procedure.51 3-Methyl-1H-pyrazole 22 (750 mg, 9.13 mmol) was dissolved in water,
KMnO4 (3.18 g, 20.1 mmol) was added and the mixture was refluxed overnight. The reaction was cooled to room
temperature, solids were filtered off, and the solvent was removed under reduced pressure. The resulting white powder
was used directly without further purification.
Ethyl 1H-pyrazole-3-carboxylate (24)
Crude 23 was dissolved in anhydrous ethanol with a catalytic amount of concentrated H2SO4 and refluxed overnight.
The reaction was allowed to cool to RT, the solvent was partially removed and the residue was neutralized using sat. aq.
NaHCO3. The aqueous phase was extracted with ethyl acetate (3x), and the combined organic layers were dried (MgSO4),
filtered and concentrated under reduced pressure, yielding the title compound as a white power (607 mg, 4.33 mmol,
47% over 2 steps). 1H NMR (400 MHz, MeOD) δ 7.73 (d, J = 2.3 Hz, 1H), 6.85 (d, J = 2.3 Hz, 1H), 4.39 (q, J = 7.1 Hz,
2H), 1.40 (t, J = 7.1 Hz, 3H). 13C NMR (101 MHz, MeOD) δ 108.84, 105.15, 61.94, 14.58.
Bis(4-fluorophenyl)(1H-pyrazol-3-yl)methanol (25)
24 (103 mg, 0.735 mmol) was dissolved in THF and cooled to 0 °C. Under vigorous stirring, a 2 M solution of 4-
fluorophenylmagnesium bromide in Et2O (1.29 mL, 2.57 mmol) was added dropwise. The reaction mixture was allowed
to warm to RT and stirred overnight. The reaction was quenched with sat. aq. NH4Cl. The aqueous phase was extracted
with DCM (3x). Combined organic layers were dried (MgSO4), filtered and concentrated under reduced pressure. The
residue was purified using silica flash chromatography (30% to 60% EtOAc in pentane) yielding the title compound as
yellowish solid (175 mg, 0.611 mmol, 83%). 1H NMR (400 MHz, CDCl3) δ 8.08 (s, 1H), 7.24 – 7.10 (m, 5H), 7.03 –
6.85 (m, 4H), 5.83 (d, J = 2.2 Hz, 1H). 13C NMR (101 MHz, MeOH) δ 162.18 (d, J = 246.8 Hz), 141.90 (d, J = 3.1 Hz),
131.77, 129.21 (d, J = 8.1 Hz), 114.90 (d, J = 21.4 Hz), 110.10, 105.43, 77.61.
Ethyl 1-trityl-1H-imidazole-4-carboxylate (27)
Ethyl 1H-imidazole-4-carboxylate 26 (100 mg, 0.714 mmol) was dissolved in DCM at 0 °C, after which trityl chloride
(199 mg, 0.713 mmol) and triethylamine (0.117 mL, 0.856 mmol) were added. The reaction mixture was allowed to
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warm up to RT overnight, after which it was quenched with water. The organic phase was separated, dried (MgSO4),
filtered and concentrated under reduced pressure, giving the title compound as a white powder (265 mg, 0.693 mmol,
97%). 1H NMR (400 MHz, CDCl3) δ 7.59 (d, J = 1.4 Hz, 1H), 7.45 (d, J = 1.4 Hz, 1H), 7.40 – 7.32 (m, 9H), 7.16 – 7.06
(m, 6H), 4.35 (q, J = 7.1 Hz, 2H), 1.37 (t, J = 7.1 Hz, 3H).
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27 (265 mg, 0.693 mmol) was dissolved in THF and cooled to 0 °C. Under vigorous stirring, a 2 M solution of 4-
fluorophenylmagnesium bromide in Et2O (1.38 mL, 2.75 mmol) was added dropwise. The reaction mixture was allowed
to warm up to RT and further stirred overnight. The reaction was quenched with sat. aq. NH4Cl. The aqueous phase was
extracted 3x with ethyl acetate. The combined organic layers were dried (MgSO4), filtered and concentrated under
reduced pressure. The residue was purified over silica column (50 % EtOAc in pentane) in order to obtain the product
as a yellowish powder (315 mg, 0.596 mmol, 86%). 1H NMR (400 MHz, CDCl3) δ 7.85 (s, 1H), 7.47 – 7.27 (m, 10H),
7.23 – 6.83 (m, 13H), 6.20 (s, 1H). 13C NMR (101 MHz, CDCl3) δ 162.18 (d, J = 246.9 Hz), 144.16, 140.79, 140.65,
129.62, 129.10 (d, J = 8.1 Hz), 128.92, 128.68, 121.17, 115.33, 115.28 – 114.61 (m), 76.24.
Bis(4-fluorophenyl)(1H-imidazol-4-yl)methanol (29)
28 (275 mg, 0.520 mmol) was dissolved in 50% TFA/DCM with a few mL of water and stirred overnight. Solvents were
removed under reduced pressure and the crude product was dissolved in diethyl ether and extracted with a 1 M aq. HCl
solution. The aqueous phase was made basic (pH > 12) with NaOH and extracted with ethyl acetate (3x). Combination,
drying (MgSO4), filtered and concentration of the organic phases afforded crude product that was of sufficient purity to
use in subsequent reactions as judged by LC/MS (83 mg, 0.29 mmol, 56%).
4-([1,1'-Biphenyl]-4-yl)-1H-1,2,3-triazole (30)
A mixture of formaldehyde (12.5 mL, 168 mmol), acetic acid (1.44 ml, 25.2 mmol) and 1,4-dioxane (125 mL) was
stirred for 15 min. Sodium azide (1.64 g, 25.2 mmol) was added, followed by 4-ethynyl-1,1'-biphenyl (3.00 g, 16.8
mmol). After 10 min, sodium ascorbate (0.667 g, 3.37 mmol), and CuSO4∙5H2O (0.210 g, 0.842 mmol) in 1 mL of water
were added. The resulting mixture was stirred for 18 h at RT. It was diluted with H2O (60 mL) and extracted with
chloroform (3x 30 mL). The combined organic layers were dried (MgSO4), filtered and concentrated. The residue was
suspended in 2 M NaOH (6 mL) and stirred for 20 h at RT. The reaction was acidified with 4 M HCl (aq.) and the white
precipitate was filtered off, yielding the desired product as a white solid (2.31 g, 10.4 mmol, 62%). 1H NMR (400 MHz,
DMSO) δ 15.18 (s, 1H), 8.40 (s, 1H), 7.99 – 7.93 (m, 2H), 7.81 – 7.75 (m, 2H), 7.75 – 7.69 (m, 2H), 7.53 – 7.45 (m,
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2H), 7.42 – 7.34 (m, 1H). 13C NMR (101 MHz, DMSO) δ 156.90, 145.31, 139.56, 128.99, 127.60, 127.17, 126.56,
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2-Benzylpyridine (5.0 mL, 31 mmol) was dissolved in ethanol (100 mL) and concentrated aqueous HCl (10 mL) was
added. Then PtO2 (112 mg, 0.49 mmol) was added and the mixture was shaken under a hydrogen atmosphere of 2 bar
at RT. After overnight shaking, solids were filtered off over celite. The solvent was removed under reduced pressure and
the residue was purified using flash column chromatography (10% methanol in DCM) to yield the title compound (4.2
g, 20 mmol, 64%). 1H NMR (300 MHz, CDCl3) δ 8.41 (s, 1H), 7.42 – 7.13 (m, 5H), 3.58 – 3.38 (m, 2H), 3.25 – 3.02
(m, 1H), 3.02 – 2.73 (m, 2H), 2.14 – 1.47 (m, 5H), 1.47 – 1.10 (m, 1H). 13C NMR (75 MHz, CDCl3) δ 136.16, 129.51,
128.76, 127.04, 58.59, 45.11, 40.07, 27.97, 22.61.
(4-([1,1'-Biphenyl]-4-yl)-1H-1,2,3-triazol-1-yl)(2-benzylpiperidin-1-yl)methanone (KT109)
Synthesized according to General Procedure 1 from 30 (2.31 g, 10.4 mmol). The N1-isomer was isolated as first eluting
isomer (621 mg, 1.47 mmol, 14%). 1H NMR (400 MHz, CDCl3) δ 7.87 (s, 2H), 7.75 – 7.60 (m, 4H), 7.53 – 7.35 (m,
4H), 7.24 (d, J = 15.7 Hz, 6H), 4.86 (s, 1H), 4.37 (d, J = 13.5 Hz, 1H), 3.31 (d, J = 52.1 Hz, 2H), 2.70 (s, 1H), 2.11 –
1.62 (m, 6H). Purity of ≥95% as determined by LC/MS (Supplementary Information).
HRMS: Calculated for [C27H26N4O + H]+ = 423.2179, found = 423.2183.
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ASSOCIATED CONTENT
Supplementary Information
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Supplementary Figures S1-7, Table S1 and Scheme S1 as mentioned in the text. LC-MS traces showing
purity of biochemically profiled final compounds. Molecular Formula Strings are submitted as comma
delimited file. This material is available free of charge via the Internet at http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding author
*E-mail: m.van.der.stelt@chem.leidenuniv.nl. Phone: (+31)71 527 4768
Author contributions
APAJ, JvH, OJMB and HD designed and performed the experiments. APAJ, JvH, OJMB, GJPvW and
MvdS interpreted the results. APAJ, OJMB, GJPvW and MvdS wrote the paper.
Notes
The authors have no conflicts of interest to declare.
ACKNOWLEDGEMENTS
A.M.C.H. van Nieuwendijk is kindly acknowledged for his advice on the synthesis and his help in the
chiral HPLC work.
ABBREVIATIONS USED
DAGL, diacylglycerol lipase; FAAH, fatty acid amide hydrolase; MAGL, monoacylglycerol lipase;
ABHD, α/β-hydrolase domain containing protein; DDHD2, DDHD domain containing protein; DIPEA,
diisopropylethylamine;
KHMDS,
potassium
bis(trimethylsilyl)
amide;
nosyl;
EDCI,
PNPB,
N-(3-
dimethylaminopropyl)-N′-ethylcarbodiimide
hydrochloride; Ns,
para-
nitrophenylbutyrate; N.D., not determined.
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